crossing96/oncoscreening huggingface dataset:
Identifying the ErbB/MAPK Signaling Cascade as a Therapeutic Target in Canine Bladder Cancer.	Transitional cell carcinoma (TCC) of the bladder comprises 2% of diagnosed canine cancers. TCC tumors are generally inoperable and unresponsive to traditional chemotherapy, indicating a need for more effective therapies. BRAF, a kinase in the mitogen-activated protein kinase (MAPK) pathway, is mutated in 70% of canine TCCs. In this study, we use BRAF mutant and wild-type TCC cell lines to characterize the role of BRAF mutations in TCC pathogenesis and assess the efficacy of inhibition of the MAPK pathway alone and in combination with other gene targets as a treatment for canine TCC. Analysis of MAPK target gene expression and assessment of extracellular signal-regulated kinase (ERK) 1/2 phosphorylation following serum starvation indicated constitutive MAPK activity in all TCC cell lines. BRAF mutant TCC cell lines were insensitive to the BRAF inhibitor vemurafenib, with IC(50) values greater than 5 μM, but exhibited greater sensitivity to a paradox-breaking BRAF inhibitor (IC(50): 0.2-1 μM). All TCC cell lines had IC(50) values less than 7 nM to the mitogen-activated protein kinase kinase (MEK) 1/2 inhibitor trametinib independent of their BRAF mutation status. ERK1/2 phosphorylation decreased after 6-hour treatments with MAPK inhibitors, but rebounded by 24 hours, suggesting the presence of resistance mechanisms. Microarray analysis identified elevated expression of the ErbB family of receptors and ligands in TCC cell lines. The pan-ErbB inhibitor sapitinib synergized with BRAF inhibition in BRAF mutant Bliley TCC cells and synergized with MEK1/2 inhibition in Bliley and BRAF wild-type Kinsey cells. These findings suggest the potential for combined MAPK and ErbB receptor inhibition as a therapy for canine TCC. SIGNIFICANCE STATEMENT: The results of this study (1) identify a novel combination strategy for canine bladder cancer treatment: targeting the ErbB/MAPK signaling cascade and (2) establish the utility of canine bladder cancer as a naturally-occurring model for human MAPK-driven cancers.	bladder
Enrichment of genes associated with squamous differentiation in cancer initiating cells isolated from urothelial cells transformed by the environmental toxicant arsenite.	Arsenic is an environmental toxicant with long-term exposure associated with the development of urothelial carcinomas. Our lab has developed an in-vitro model of urothelial carcinoma by exposing the immortal, but non-tumorigenic bladder cell line, the UROtsa, to arsenite (As(3+)). These transformed cells form tumors in immune-compromised mice, which resemble urothelial carcinomas with components of the tumor exhibiting squamous differentiation. The goal of the present study was to determine the differences in global gene expression patterns between the As(3+)-transformed UROtsa cells and the urospheres (spheroids containing putative cancer initiating cells) isolated from these cell lines and to determine if the genes involved in the development of squamous differentiation were enriched in the urospheres. The results obtained in this study show an enrichment of genes such as KRT1, KRT5, KRT6A, KRT6B, KRT6C, KRT14 and KRT16 associated with squamous differentiation, a characteristic feature seen in aggressive basal subtypes of urothelial cell carcinoma (UCC) in the urospheres isolated from As(3+)-transformed UROtsa cells. In addition, there is increased expression of several of the small proline-rich proteins (SPRR) in the urospheres and overexpression of these genes occur in UCC's displaying squamous differentiation. In conclusion, the cancer initiating cells present in the urospheres are enriched with genes associated with squamous differentiation.	bladder
Correlation of BRCA2 gene mutation and prognosis as well as variant genes in invasive urothelial carcinoma of the bladder.	BACKGROUND: This study aimed to investigate the correlation of BRCA2 gene mutation and prognosis as well as variant genes in patients with invasive urothelial carcinoma of the bladder. It predicted and explored the possible mechanism and clinical value of BRCA2 in the occurrence and development of tumors. METHODS: Data sets of patients with bladder cancer were collected from the Cancer Genome Atlas (TCGA) database. Also the gene expression profile data and clinical information of the BRCA2 mutation group and non-BRCA2 mutation group were downloaded. RESULTS: The prognosis of the BRCA2 mutation group was better than that of the non-mutant group. Among the down-regulated genes, the following genes showed significant differences between the two groups: CCL22, CYP2B6, CYP2E1, CYP4F2, HTR1E, HTR1F, KLRC1, NAPSA, SELL, SFTPA1, SFTPA2, SFTPB, SFTPC and STRA8, while the following genes among the up-regulated genes showed significant differences between the two groups: ELAVL3, NOTUM, TRH and VIP. Meanwhile, the following gene sets were highly enriched in BRCA2: cell cycle, DNA replication, homologous recombination, oocyte meiosis, ubiquitin-mediated proteolysis, base excision repair, progestin mediated oocyte maturation, basal transcription factor, biosynthesis of N polysaccharide, mismatch repair, sliceosome, purine metabolism as well as P53 and neurotrophic factor signaling pathway, etc.CONCLUSION: These findings suggested that the BRCA2 gene mutation is a good prognostic factor and can be used as a gene to predict the prognosis in the bladder cancer patients.	bladder
lncRNA CCAT1 promotes bladder cancer cell proliferation, migration and invasion.	OBJECTIVE: To study the expression patterns of long noncoding RNA (lncRNA) colon cancer-associated transcript 1 (CCAT1) and the changes in cell proliferation, apoptosis, migration and invasion induced by silencing CCAT1 in bladder cancer cells. MATERIALS AND METHODS: The expression levels of CCAT1 were determined using realtime quantitative polymerase chain reaction in cancerous tissues and paired normal tissues from 34 patients with bladder cancer. The relationship between clinical characteristics and CCAT1 expression was analyzed. And then we conducted cell experiments. Bladder urothelial carcinoma cell lines T24 and 5637 cells were transfected with CCAT1 small interfering RNA (siRNA) or scramble siRNA. Cell proliferation and apoptosis changes were determined using a Cell Counting Kit-8 (CCK-8) assay and a fl ow cytometry assay. Migration and invasion changes were measured using a wound healing assay and a trans-well assay. microRNAs (miRNAs) were predicted by Starbase 2.0, and their differential expression levels were studied. RESULTS: CCAT1 was signifi cantly upregulated in bladder cancer (P < 0.05). CCAT1 upregulation was positively related to tumor stage (P = 0.004), tumor grade (P = 0.001) and tumor size (P = 0.042). Cell proliferation, migration and invasion were promoted by abnormally expressed CCAT1. miRNAs miR-181b-5p, miR-152-3p, miR-24-3p, miR-148a-3p and miR-490-3p were potentially related to the aforementioned functions of CCAT1. CONCLUSION: CCAT1 plays an oncogenic role in urothelial carcinoma of the bladder. In addition, CCAT1 may be a potential therapeutic target in this cancer.	bladder
Epigenetic regulation of mammalian Hedgehog signaling to the stroma determines the molecular subtype of bladder cancer.	In bladder, loss of mammalian Sonic Hedgehog (Shh) accompanies progression to invasive urothelial carcinoma, but the molecular mechanisms underlying this cancer-initiating event are poorly defined. Here, we show that loss of Shh results from hypermethylation of the CpG shore of the Shh gene, and that inhibition of DNA methylation increases Shh expression to halt the initiation of murine urothelial carcinoma at the early stage of progression. In full-fledged tumors, pharmacologic augmentation of Hedgehog (Hh) pathway activity impedes tumor growth, and this cancer-restraining effect of Hh signaling is mediated by the stromal response to Shh signals, which stimulates subtype conversion of basal to luminal-like urothelial carcinoma. Our findings thus provide a basis to develop subtype-specific strategies for the management of human bladder cancer.	bladder
Organ-preserving approach via radiotherapy for small cell carcinoma of the bladder: an analysis based on the Japanese Radiation Oncology Study Group (JROSG) survey.	Small cell carcinoma of the bladder is extremely rare, accounting for <1% of all malignant tumours in the urinary tract. Thus, no standard therapy modality for this malignancy has been established. This study aimed to retrospectively analyse the clinical outcomes associated with definitive radiotherapy for small cell carcinoma of the bladder. A questionnaire-based survey of patients with pathologically proven small cell carcinoma of the bladder treated with definitive radiation therapy between 1990 and 2010 was conducted by the Japanese Radiation Oncology Study Group. The clinical records of 12 eligible patients were collected from nine institutions. The median age of the patients was 70.5 years (range: 44-87 years), and the median follow-up period was 27.3 months (range: 3.3-117.8 months). The median prescribed dose was 60 Gy (range: 50.0-61.0 Gy), and a median of 2.0 Gy (range: 1.2-2.0 Gy) was administered per fraction. Systemic chemotherapy combined with radiotherapy was performed in eight cases (66.7%). The 3- and 5-year overall survival rates were 50.0% and 33.3%, respectively. And the 3- and 5-year local control rates were 66.7% and 55.6%, respectively. Chemotherapy significantly improved overall survival and relapse-free survival (P = 0.006 and 0.001, respectively). No serious adverse events occurred in the observation period. All patients who achieved local control maintained functional bladders. In conclusion, radiotherapy is a potential local treatment option and has an important role in maintaining quality of life. Systemic chemotherapy combined with local radiotherapy seems to be effective in improving survival.	bladder
BCG-induced discitis and osteomyelitis in a patient with a history of bladder cancer.	This article describes the diagnosis and treatment of a patient with lumbar discitis and osteomyelitis caused by Bacillus Calmette-Guérin instillation therapy for treatment of superficial bladder cancer. Treatment of this rare condition consists of antituberculosis microbial therapy and one or more IV antibiotics to cover multidrug-resistant bacteria in the bone.	bladder
Examination of Diagnostic Accuracy of UroVysion Fluorescence In Situ Hybridization for Bladder Cancer in a Single Community of Japanese Hospital Patients.	Objective: UroVysion (Abbott Molecular, Inc., Illinois, USA) is based on multicolor fluorescence in situ hybridization (FISH). It has been used successfully in the USA following its Food and Drug Administration approval in 2001. However, the technology was not approved for use in Japan until 2017. Cystoscopy and urine cytology are the most frequently used examinations to detect bladder cancer in Japan, and there are only a few reports regarding the performance of UroVysion. Therefore, the aim of this study is to examine the diagnostic accuracy of UroVysion FISH in Japanese patients whose tumors are detected by cystoscopy before transurethral resection of bladder tumor (TURBT). Methods: From April 2018 to July 2018, a total of 40 patients who were diagnosed as having bladder tumors by cystoscopy, and therefore underwent TURBT were registered in this study. One day before TURBT, urine cytology and UroVysion FISH were used in order to compare the accuracy with which they could detect bladder carcinoma, as confirmed by pathological results of TURBT. Results: The pathological results of TURBT showed urothelial carcinoma in 33 cases. Urine cytology showed positive results for 0 cases (0%), suspicious results for 10 cases (30.3%), and negative results for 23 cases (69.7%). On the other hand, UroVysion FISH indicated 9 positive cases (27.3%) and 24 negative cases (72.7%). There were 19 cases of urothelial carcinoma (57.6%) that were not detected by either method. Conclusion: We conclude that UroVysion FISH alone is insufficient to detect bladder cancer and that cystoscopy is essential for the optimum detection or follow up of bladder cancer cases in our hospital.	bladder
Individual patient risk of progression of urinary bladder papillary tumors estimated from biomarkers at initial transurethral resection of bladder tumor.	OBJECTIVE: To determine if individual, instead of group, patient progression risk could be predicted using p53, Ki67 and CK20 biomarker percentage values at initial transurethral resection of bladder tumor specimens. METHODS: This was an observational study where biomarkers were measured with no knowledge of tumor outcome. Initial bladder tumor specimens were classified as non-invasive and invasive to sub-epithelium (pT1). Percentages of stained biomarker cells were tested as progression predictors from non-invasive to pT1 and pT1 to pT2. Progression probability was correlated with biomarker percentages resulting in a regression equation. RESULTS: We studied 112 patients (median age = 67, range 37-91, males 83/112 (73%), with median follow-up of 39 months (range 1.7-140). Mean biomarker values were higher in stage pT1 than in non-invasive (all p < 0.001). Cut-off points separating progression from non-progression groups in stage pT1 were higher than in non-invasive for all biomarkers. Correlation R values for progression probability vs. biomarker percentages varied from 0.7 to 0.9 (all p < 0.001), regression slopes from 0.1 to 0.8 and intercepts from 11 to 35. A novel individual progression probability was calculated as the product of biomarker percentage of stained cells and slope, plus the prevalence-adjusted intercept. CONCLUSIONS: Identification of individual risk of progression in patients with non-muscle-invasive bladder tumors was possible using p53- and Ki67-derived progression probability using a regression equation. Combining biomarker-derived progression probability to tumor stage pT1 improves progression to pT2 predictive accuracy.	bladder
The prognostic impact of hexaminolevulinate-based bladder tumor resection in patients with primary non-muscle invasive bladder cancer treated with radical cystectomy.	PURPOSE: To investigate whether hexaminolevulinate-based (HAL) bladder tumor resection (TURBT) impacts on outcomes of patients with primary non-muscle-invasive bladder cancer (NMIBC) who were eventually treated with radical cystectomy (RC). METHODS: A total of 131 consecutive patients exhibiting NMIBC at primary diagnosis were retrospectively investigated whether they had undergone any HAL-guided TURBT prior to RC. Uni- and multivariable analyses were used to evaluate the impact of HAL-TURBT on cancer-specific (CSS) and overall survival (OS). The median follow-up was 38 months (IQR 13-56). RESULTS: Of the 131 patients, 69 (52.7%) were managed with HAL- and 62 (47.3%) with white light (WL)-TURBT only prior to RC. HAL-TURBT was associated with a higher number of TURBTs prior to RC (p = 0.002) and administration of intravesical chemotherapy (p = 0.043). A trend towards a higher rate of tumor-associated immune cell infiltrates in RC specimens (p = 0.07) and a lower utilization rate of post-operative systemic chemotherapy (p = 0.10) was noted for patients who were treated with HAL-TURBT. The 5-year CSS/OS was 90.9%/74.5% for the HAL-group and 73.8%/55.8% for the WL-group (p = 0.042/0.038). In multivariable analysis, lymph node tumor involvement (p = 0.007), positive surgical margins (p = 0.001) and performance of WL-TURBT only (p = 0.040) were independent predictors for cancer-specific death. CONCLUSIONS: The present data suggest that the resection of NMIBC under HAL exerts a beneficial impact on outcomes of patients who will need to undergo RC during their course of disease. This finding may be due to improved risk stratification as the resection under HAL may allow more patients to be treated timely and adequately.	bladder
Simultaneous determination of seven endogenous aldehydes in human blood by headspace gas chromatography-mass spectrometry.	Endogenous aldehydes (EAs) formed by the free-radical-mediated reaction are regarded as potential biological markers of several diseases. In this work, an automated and solvent-free analytical method was developed for quantitative analysis of seven EAs (C1-C7) in human blood by using gas chromatography-mass spectrometry coupled with a headspace generator sampler (HS-GC-MS). A 1:4 (blood:water) dilution and the 1,2‑dibromopropane internal standard were introduced to reduce the influence of the matrix effect from complex biological fluids. The sample preparation steps were simplified. Various experimental parameters for derivatization and extraction conditions were studied such as HS extraction temperature and time, the amount of derivatization reagent, pH and the salt effect. Under these optimum conditions, seven low-mass aldehydes were separated and analyzed within 10 min. Additionally, this method achieved limits of detection in the range of 0.0692-0.864 μg/L, an excellent linearity with correlation coefficients higher than 0.9996 and appropriate repeatability and reproducibility values (RSD < 12% at low, middle and high levels). The HS-GC-MS method was applied to measure the concentrations of the seven aldehydes in blood from bladder cancer patients (n = 15) and control subjects (n = 15). Compared with the control subjects, the levels of butanal (p < 0.01), formaldehyde, acetaldehyde, propanal, pentanal, hexanal and heptanal (all p < 0.001) were increased significantly, indicating that EAs may be useful as biomarkers in the early diagnosis of bladder cancer.	bladder
Increased expression of DCLK1, a novel putative CSC maker, is associated with tumor aggressiveness and worse disease-specific survival in patients with bladder carcinomas.	Doublecortin-like kinase 1 (DCLK1) has been characterized as a novel potential cancer stem cell (CSC) marker in several types of cancer. It is considered as one of the most specific markers for distinguishing colorectal CSCs from normal stem cells. Yet, there are limited reports on the role of DCLK1 as a putative CSC marker in bladder cancer. Using immunohistochemistry, DCLK1 expression was examined in a well-defined tissue microarray series of 472 bladder cancer tissues. The association between DCLK1 protein expression and clinicopathological features, as well as survival outcomes, was assessed. Our findings showed strong, moderate, and weak DCLK1 expression in 123 (26.1%), 230 (48.7%), and 119 (25.2%) of the bladder cancer specimens, respectively. Higher expression of DCLK1 was significantly associated with increase in histological grade (P ≤ .001), pT stage (P = .014), lamina propria (P = .006), and lamina propria/muscularis (L/M) involvement (P = .014). On multivariate analysis, pT stage (P < .001), histological grade (P = .021), and lamina propria involvement (P = .001) were independent prognostic factors in DCLK1 expression. Moreover, the expression of DCLK1 was found to be an independent marker of poor prognosis for disease- specific survival (DSS) (P = .048) in bladder carcinomas. Our observations showed that DCLK1 expression was associated with more aggressive tumor behavior, more advanced disease, and poorer DSS in patients with bladder carcinomas. However, any potential clinical applications of DCLK1 as a novel target molecule in bladder cancer patients would require further investigations.	bladder
The encouraging role of long noncoding RNA small nuclear RNA host gene 16 in epithelial-mesenchymal transition of bladder cancer via directly acting on miR-17-5p/metalloproteinases 3 axis.	The present investigation was intended to elucidate whether long noncoding RNA small nuclear RNA host gene 16 (SNHG16) could regulate the epithelial-mesenchymal transition process of bladder cancer cells by directing expressions of miR-17-5p and metalloproteinases 3 (TIMP3). To elucidate the point, we collected 275 pairs of bladder cancer tissues and corresponding adjacent normal tissues, as well as four bladder cancer cell lines and the normal human bladder epithelial cell line. Moreover, pcDNA3.1-SNHG16, si-SNHG16, miR-17-5p mimic, miR-17-5p inhibitor, pcDNA3.1-TIMP3, and si-TIMP3 were prepared for transfection, and CCK-8 assay, colony formation assay, flow cytometry, wound healing assay, and transwell assay were carried out. Finally, the dual luciferase reporter gene assay was performed to figure out whether targeted regulations were present among SNHG16, miR-17-5p, and TIMP3. The laboratory findings demonstrated that the bladder cancer patients carrying under-expressed SNHG16 or miR-17-5p were associated with extended survival time when compared with those possessing overexpressed SNHG16 and miR-17-5p (P < 0.05). Furthermore, overexpression of SNHG16 and miR-17-5p both enhanced the viability, proliferation, migration, and invasion (P < 0.05), and simultaneously suppressed their apoptosis (P < 0.05). Transfections of pcDNA3.1-SNHG16 and si-SNHG16, respectively, resulted in overexpression and under-expression of miR-17-5p, and the dual luciferase reporter gene assay demonstrated a targeted relationship between SNHG16 and miR-17-5p (P < 0.05). Besides, the expression of TIMP3 was subjected to targeted regulation of miR-17-5p (P < 0.05), and its overexpression could reverse the effects of miR-17-5p on proliferation and metastasis (P < 0.05). Conclusively, purposeful modification of SNHG16/miR-17-5p/TIMP3 signaling might be conducive to postpone the aggravation of bladder cancer.	bladder
Coffee and tea drinking and risk of cancer of the urinary tract in male smokers.	PURPOSE: We evaluated the association of coffee and tea drinking with risk of the urinary tract cancer in Finnish men, with high coffee consumption, using data from the Alpha-Tocopherol, Beta-Carotene Cancer Prevention (ATBC) Study. METHODS: The ATBC trial conducted from 1985 to 1993 enrolled 29,133 male smokers. We used Cox proportional hazards regression models to estimate hazard ratios (HRs) and confidence intervals (CIs), using men who drank more than 0 but less than 1 cup coffee/d and tea nondrinkers as our referent group for coffee and tea analyses, respectively. RESULTS: During 472,402 person-years of follow-up, 835 incident cases of bladder cancer and 366 cases of renal cell carcinoma were ascertained. For bladder cancer, we observed no association for coffee consumption (HR ≥4 vs. >0 to <1 cups/d = 1.16, 95% CI = 0.86-1.56) and a borderline statistically significant inverse association for tea consumption (HR ≥1 vs. 0 cup/d = 0.77, 95% CI = 0.58-1.00). For renal cell carcinoma, we observed no association for coffee (HR ≥4 vs. >0 to <1 cups/d = 0.85, 95% CI = 0.55-1.32) or tea consumption (HR ≥1 vs. 0 cup/d = 1.00, 95% CI = 0.68-1.46). We found no impact of coffee preparation on coffee-cancer associations. CONCLUSIONS: Coffee drinking was not associated with urinary tract cancers risk. Further research on tea and bladder cancer is warranted.	bladder
Galectins in prostate and bladder cancer: tumorigenic roles and clinical opportunities.	Advanced prostate and bladder cancer are two outstanding unmet medical needs for urological oncologists. The high prevalence of these tumours, lack of effective biomarkers and limited effective treatment options highlight the importance of basic research in these diseases. Galectins are a family of β-galactoside-binding proteins that are frequently altered (upregulated or downregulated) in a wide range of tumours and have roles in different stages of tumour development and progression, including immune evasion. In particular, altered expression levels of different members of the galectin family have been reported in prostate and bladder cancers, which, together with the aberrant glycosylation patterns found in tumour cells and the constituent cell types of the tumour microenvironment, can result in malignant transformation and tumour progression. Understanding the roles of galectin family proteins in the development and progression of prostate and bladder cancer could yield key insights to inform the clinical management of these diseases.	bladder